1
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. Structure 2024; 32:1528-1543.e3. [PMID: 39025067 PMCID: PMC11380583 DOI: 10.1016/j.str.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/30/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters, the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Samuel P Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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2
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Kok M, Brodsky JL. The biogenesis of potassium transporters: implications of disease-associated mutations. Crit Rev Biochem Mol Biol 2024:1-45. [PMID: 38946646 DOI: 10.1080/10409238.2024.2369986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/16/2024] [Indexed: 07/02/2024]
Abstract
The concentration of intracellular and extracellular potassium is tightly regulated due to the action of various ion transporters, channels, and pumps, which reside primarily in the kidney. Yet, potassium transporters and cotransporters play vital roles in all organs and cell types. Perhaps not surprisingly, defects in the biogenesis, function, and/or regulation of these proteins are linked to range of catastrophic human diseases, but to date, few drugs have been approved to treat these maladies. In this review, we discuss the structure, function, and activity of a group of potassium-chloride cotransporters, the KCCs, as well as the related sodium-potassium-chloride cotransporters, the NKCCs. Diseases associated with each of the four KCCs and two NKCCs are also discussed. Particular emphasis is placed on how these complex membrane proteins fold and mature in the endoplasmic reticulum, how non-native forms of the cotransporters are destroyed in the cell, and which cellular factors oversee their maturation and transport to the cell surface. When known, we also outline how the levels and activities of each cotransporter are regulated. Open questions in the field and avenues for future investigations are further outlined.
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Affiliation(s)
- Morgan Kok
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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3
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Rioux AV, Nsimba-Batomene TR, Slimani S, Bergeron NAD, Gravel MAM, Schreiber SV, Fiola MJ, Haydock L, Garneau AP, Isenring P. Navigating the multifaceted intricacies of the Na +-Cl - cotransporter, a highly regulated key effector in the control of hydromineral homeostasis. Physiol Rev 2024; 104:1147-1204. [PMID: 38329422 PMCID: PMC11381001 DOI: 10.1152/physrev.00027.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/01/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024] Open
Abstract
The Na+-Cl- cotransporter (NCC; SLC12A3) is a highly regulated integral membrane protein that is known to exist as three splice variants in primates. Its primary role in the kidney is to mediate the cosymport of Na+ and Cl- across the apical membrane of the distal convoluted tubule. Through this role and the involvement of other ion transport systems, NCC allows the systemic circulation to reclaim a fraction of the ultrafiltered Na+, K+, Cl-, and Mg+ loads in exchange for Ca2+ and [Formula: see text]. The physiological relevance of the Na+-Cl- cotransport mechanism in humans is illustrated by several abnormalities that result from NCC inactivation through the administration of thiazides or in the setting of hereditary disorders. The purpose of the present review is to discuss the molecular mechanisms and overall roles of Na+-Cl- cotransport as the main topics of interest. On reading the narrative proposed, one will realize that the knowledge gained in regard to these themes will continue to progress unrelentingly no matter how refined it has now become.
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Affiliation(s)
- A V Rioux
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - T R Nsimba-Batomene
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - S Slimani
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - N A D Bergeron
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - M A M Gravel
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - S V Schreiber
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - M J Fiola
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
| | - L Haydock
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
- Service de Néphrologie-Transplantation Rénale Adultes, Hôpital Necker-Enfants Malades, AP-HP, INSERM U1151, Université Paris Cité, Paris, France
| | - A P Garneau
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
- Service de Néphrologie-Transplantation Rénale Adultes, Hôpital Necker-Enfants Malades, AP-HP, INSERM U1151, Université Paris Cité, Paris, France
| | - P Isenring
- Department of Medicine, Nephrology Research Group, Laval University, Quebec City, Quebec, Canada
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4
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Zhang S, Meor Azlan NF, Josiah SS, Zhou J, Zhou X, Jie L, Zhang Y, Dai C, Liang D, Li P, Li Z, Wang Z, Wang Y, Ding K, Wang Y, Zhang J. The role of SLC12A family of cation-chloride cotransporters and drug discovery methodologies. J Pharm Anal 2023; 13:1471-1495. [PMID: 38223443 PMCID: PMC10785268 DOI: 10.1016/j.jpha.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
The solute carrier family 12 (SLC12) of cation-chloride cotransporters (CCCs) comprises potassium chloride cotransporters (KCCs, e.g. KCC1, KCC2, KCC3, and KCC4)-mediated Cl- extrusion, and sodium potassium chloride cotransporters (N[K]CCs, NKCC1, NKCC2, and NCC)-mediated Cl- loading. The CCCs play vital roles in cell volume regulation and ion homeostasis. Gain-of-function or loss-of-function of these ion transporters can cause diseases in many tissues. In recent years, there have been considerable advances in our understanding of CCCs' control mechanisms in cell volume regulations, with many techniques developed in studying the functions and activities of CCCs. Classic approaches to directly measure CCC activity involve assays that measure the transport of potassium substitutes through the CCCs. These techniques include the ammonium pulse technique, radioactive or nonradioactive rubidium ion uptake-assay, and thallium ion-uptake assay. CCCs' activity can also be indirectly observed by measuring γ-aminobutyric acid (GABA) activity with patch-clamp electrophysiology and intracellular chloride concentration with sensitive microelectrodes, radiotracer 36Cl-, and fluorescent dyes. Other techniques include directly looking at kinase regulatory sites phosphorylation, flame photometry, 22Na+ uptake assay, structural biology, molecular modeling, and high-throughput drug screening. This review summarizes the role of CCCs in genetic disorders and cell volume regulation, current methods applied in studying CCCs biology, and compounds developed that directly or indirectly target the CCCs for disease treatments.
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Affiliation(s)
- Shiyao Zhang
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
| | - Nur Farah Meor Azlan
- Institute of Biomedical and Clinical Sciences, Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4PS, UK
| | - Sunday Solomon Josiah
- Institute of Biomedical and Clinical Sciences, Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4PS, UK
| | - Jing Zhou
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaoxia Zhou
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
| | - Lingjun Jie
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
| | - Yanhui Zhang
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
| | - Cuilian Dai
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
| | - Dong Liang
- Aurora Discovery Inc., Foshan, Guangdong, 528300, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, Shandong, 266021, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Zhen Wang
- State Key Laboratory of Chemical Biology, Research Center of Chemical Kinomics, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yun Wang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Research Center of Chemical Kinomics, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan Wang
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
| | - Jinwei Zhang
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 363001, China
- Institute of Biomedical and Clinical Sciences, Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4PS, UK
- State Key Laboratory of Chemical Biology, Research Center of Chemical Kinomics, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
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5
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Trejo F, Elizalde S, Mercado A, Gamba G, de losHeros P. SLC12A cryo-EM: analysis of relevant ion binding sites, structural domains, and amino acids. Am J Physiol Cell Physiol 2023; 325:C921-C939. [PMID: 37545407 DOI: 10.1152/ajpcell.00089.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
The solute carrier family 12A (SLC12A) superfamily of membrane transporters modulates the movement of cations coupled with chloride across the membrane. In doing so, these cotransporters are involved in numerous aspects of human physiology: cell volume regulation, ion homeostasis, blood pressure regulation, and neurological action potential via intracellular chloride concentration modulation. Their physiological characterization has been largely studied; however, understanding the mechanics of their function and the relevance of structural domains or specific amino acids has been a pending task. In recent years, single-particle cryogenic electron microscopy (cryo-EM) has been successfully applied to members of the SLC12A family including all K+:Cl- cotransporters (KCCs), Na+:K+:2Cl- cotransporter NKCC1, and recently Na+:Cl- cotransporter (NCC); revealing structural elements that play key roles in their function. The present review analyzes the data provided by these cryo-EM reports focusing on structural domains and specific amino acids involved in ion binding, domain interactions, and other important SCL12A structural elements. A comparison of cryo-EM data from NKCC1 and KCCs is presented in the light of the two recent NCC cryo-EM studies, to propose insight into structural elements that might also be found in NCC and are necessary for its proper function. In the final sections, the importance of key coordination residues for substrate specificity and their implication on various pathophysiological conditions and genetic disorders is reviewed, as this could provide the basis to correlate structural elements with the development of novel and selective treatments, as well as mechanistic insight into the function and regulation of cation-coupled chloride cotransporters (CCCs).
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Affiliation(s)
- Fátima Trejo
- Unidad de Investigación UNAM-INC, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stephanie Elizalde
- Departamento de Nefrología y Metabolismo Mineral, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Adriana Mercado
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Gerardo Gamba
- Departamento de Nefrología y Metabolismo Mineral, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Molecular Physiology Unit, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Paola de losHeros
- Unidad de Investigación UNAM-INC, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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6
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Modi AD, Khan AN, Cheng WYE, Modi DM. KCCs, NKCCs, and NCC: Potential targets for cardiovascular therapeutics? A comprehensive review of cell and region specific expression and function. Acta Histochem 2023; 125:152045. [PMID: 37201245 DOI: 10.1016/j.acthis.2023.152045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023]
Abstract
Cardiovascular diseases, the leading life-threatening conditions, involve cardiac arrhythmia, coronary artery disease, myocardial infarction, heart failure, cardiomyopathy, and heart valve disease that are associated with the altered functioning of cation-chloride cotransporters. The decreased number of cation-chloride cotransporters leads to reduced reactivity to adrenergic stimulation. The KCC family is crucial for numerous physiological processes including cell proliferation and invasion, regulation of membrane trafficking, maintaining ionic and osmotic homeostasis, erythrocyte swelling, dendritic spine formation, maturation of postsynaptic GABAergic inhibition, and inhibitory/excitatory signaling in neural tracts. KCC2 maintains intracellular chlorine homeostasis and opposes β-adrenergic stimulation-induced Cl- influx to prevent arrhythmogenesis. KCC3-inactivated cardiac tissue shows increased vascular resistance, aortic distensibility, heart size and weight (i.e. hypertrophic cardiomyopathy). Due to KCC4's high affinity for K+, it plays a vital role in cardiac ischemia with increased extracellular K+. The NKCC and NCC families play a vital role in the regulation of saliva volume, establishing the potassium-rich endolymph in the cochlea, sodium uptake in astrocytes, inhibiting myogenic response in microcirculatory beds, regulation of smooth muscle tone in resistance vessels, and blood pressure. NKCC1 regulates chlorine homeostasis and knocking it out impairs cardiomyocyte depolarization and cardiac contractility as well as impairs depolarization and contractility of vascular smooth muscle rings in the aorta. The activation of NCC in vascular cells promotes the formation of the abdominal aortic aneurysm. This narrative review provides a deep insight into the structure and function of KCCs, NKCCs, and NCC in human physiology and cardiac pathobiology. Also, it provides cell-specific (21 cell types) and region-specific (6 regions) expression of KCC1, KCC2, KCC3, KCC4, NKCC1, NKCC2, and NCC in heart.
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Affiliation(s)
- Akshat D Modi
- Department of Biological Sciences, University of Toronto, Scarborough, Ontario M1C 1A4, Canada; Department of Genetics and Development, Krembil Research Institute, Toronto, Ontario M5T 0S8, Canada.
| | - Areej Naim Khan
- Department of Human Biology, University of Toronto, Toronto, Ontario M5S 3J6, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wing Yan Elizabeth Cheng
- Department of Neuroscience, University of Toronto, Scarborough, Ontario M1C 1A4, Canada; Department of Biochemistry, University of Toronto, Scarborough, Ontario M1C 1A4, Canada
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7
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Moreno E, Pacheco-Alvarez D, Chávez-Canales M, Elizalde S, Leyva-Ríos K, Gamba G. Structure-function relationships in the sodium chloride cotransporter. Front Physiol 2023; 14:1118706. [PMID: 36998989 PMCID: PMC10043231 DOI: 10.3389/fphys.2023.1118706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
The thiazide sensitive Na+:Cl− cotransporter (NCC) is the principal via for salt reabsorption in the apical membrane of the distal convoluted tubule (DCT) in mammals and plays a fundamental role in managing blood pressure. The cotransporter is targeted by thiazide diuretics, a highly prescribed medication that is effective in treating arterial hypertension and edema. NCC was the first member of the electroneutral cation-coupled chloride cotransporter family to be identified at a molecular level. It was cloned from the urinary bladder of the Pseudopleuronectes americanus (winter flounder) 30 years ago. The structural topology, kinetic and pharmacology properties of NCC have been extensively studied, determining that the transmembrane domain (TM) coordinates ion and thiazide binding. Functional and mutational studies have discovered residues involved in the phosphorylation and glycosylation of NCC, particularly on the N-terminal domain, as well as the extracellular loop connected to TM7-8 (EL7-8). In the last decade, single-particle cryogenic electron microscopy (cryo-EM) has permitted the visualization of structures at high atomic resolution for six members of the SLC12 family (NCC, NKCC1, KCC1-KCC4). Cryo-EM insights of NCC confirm an inverted conformation of the TM1-5 and TM6-10 regions, a characteristic also found in the amino acid-polyamine-organocation (APC) superfamily, in which TM1 and TM6 clearly coordinate ion binding. The high-resolution structure also displays two glycosylation sites (N-406 and N-426) in EL7-8 that are essential for NCC expression and function. In this review, we briefly describe the studies related to the structure-function relationship of NCC, beginning with the first biochemical/functional studies up to the recent cryo-EM structure obtained, to acquire an overall view enriched with the structural and functional aspects of the cotransporter.
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Affiliation(s)
- Erika Moreno
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - María Chávez-Canales
- Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez and Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stephanie Elizalde
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Karla Leyva-Ríos
- Escuela de Medicina, Universidad Panamericana, Mexico City, Mexico
| | - Gerardo Gamba
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Molecular Phisiology Unit, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Gerardo Gamba,
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8
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Fan M, Zhang J, Lee CL, Zhang J, Feng L. Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter. Nature 2023; 614:788-793. [PMID: 36792826 PMCID: PMC10030352 DOI: 10.1038/s41586-023-05718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023]
Abstract
The sodium-chloride cotransporter (NCC) is critical for kidney physiology1. The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron2,3, and mutations in the NCC cause the salt-wasting disease Gitelman syndrome4. As a key player in salt handling, the NCC regulates blood pressure and is the target of thiazide diuretics, which have been widely prescribed as first-line medications to treat hypertension for more than 60 years5-7. Here we determined the structures of human NCC alone and in complex with a commonly used thiazide diuretic using cryo-electron microscopy. These structures, together with functional studies, reveal major conformational states of the NCC and an intriguing regulatory mechanism. They also illuminate how thiazide diuretics specifically interact with the NCC and inhibit its transport function. Our results provide critical insights for understanding the Na-Cl cotransport mechanism of the NCC, and they establish a framework for future drug design and for interpreting disease-related mutations.
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Affiliation(s)
- Minrui Fan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jianxiu Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chien-Ling Lee
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinru Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Zhao Y, Cao E. Structural Pharmacology of Cation-Chloride Cotransporters. MEMBRANES 2022; 12:1206. [PMID: 36557113 PMCID: PMC9784483 DOI: 10.3390/membranes12121206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Loop and thiazide diuretics have been cornerstones of clinical management of hypertension and fluid overload conditions for more than five decades. The hunt for their molecular targets led to the discovery of cation-chloride cotransporters (CCCs) that catalyze electroneutral movement of Cl- together with Na+ and/or K+. CCCs consist of two 1 Na+-1 K+-2 Cl- (NKCC1-2), one 1 Na+-1 Cl- (NCC), and four 1 K+-1 Cl- (KCC1-4) transporters in human. CCCs are fundamental in trans-epithelia ion secretion and absorption, homeostasis of intracellular Cl- concentration and cell volume, and regulation of neuronal excitability. Malfunction of NKCC2 and NCC leads to abnormal salt and water retention in the kidney and, consequently, imbalance in electrolytes and blood pressure. Mutations in KCC2 and KCC3 are associated with brain disorders due to impairments in regulation of excitability and possibly cell volume of neurons. A recent surge of structures of CCCs have defined their dimeric architecture, their ion binding sites, their conformational changes associated with ion translocation, and the mechanisms of action of loop diuretics and small molecule inhibitors. These breakthroughs now set the stage to expand CCC pharmacology beyond loop and thiazide diuretics, developing the next generation of diuretics with improved potency and specificity. Beyond drugging renal-specific CCCs, brain-penetrable therapeutics are sorely needed to target CCCs in the nervous system for the treatment of neurological disorders and psychiatric conditions.
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10
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Nan J, Yuan Y, Yang X, Shan Z, Liu H, Wei F, Zhang W, Zhang Y. Cryo-EM structure of the human sodium-chloride cotransporter NCC. SCIENCE ADVANCES 2022; 8:eadd7176. [PMID: 36351028 PMCID: PMC9645730 DOI: 10.1126/sciadv.add7176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/21/2022] [Indexed: 05/29/2023]
Abstract
The sodium-chloride cotransporter NCC mediates the coupled import of sodium and chloride across the plasma membrane, playing vital roles in kidney extracellular fluid volume and blood pressure control. Here, we present the full-length structure of human NCC, with 2.9 Å for the transmembrane domain and 3.8 Å for the carboxyl-terminal domain. NCC adopts an inward-open conformation and a domain-swap dimeric assembly. Conserved ion binding sites among the cation-chloride cotransporters and the Na2 site are observed in our structure. A unique His residue in the substrate pocket in NCC potentially interacts with Na1 and Cl1 and might also mediate the coordination of Na2 through a Ser residue. Putative observed water molecules are indicated to participate in the coordination of ions and TM coupling. Together with transport activity assays, our structure provides the first glimpse of NCC and defines ion binding sites, promoting drug development for hypertension targeting on NCC.
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Affiliation(s)
- Jing Nan
- Shanghai Fifth People’s Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yafei Yuan
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuemei Yang
- Shanghai Fifth People’s Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ziyang Shan
- Shanghai Fifth People’s Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Huihui Liu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China
| | - Feiwen Wei
- Shanghai Fifth People’s Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Zhang
- Shanghai Fifth People’s Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yanqing Zhang
- Shanghai Fifth People’s Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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11
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Neumann C, Rosenbæk LL, Flygaard RK, Habeck M, Karlsen JL, Wang Y, Lindorff‐Larsen K, Gad HH, Hartmann R, Lyons JA, Fenton RA, Nissen P. Cryo-EM structure of the human NKCC1 transporter reveals mechanisms of ion coupling and specificity. EMBO J 2022; 41:e110169. [PMID: 36239040 PMCID: PMC9713717 DOI: 10.15252/embj.2021110169] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 12/03/2022] Open
Abstract
The sodium-potassium-chloride transporter NKCC1 of the SLC12 family performs Na+ -dependent Cl- - and K+ -ion uptake across plasma membranes. NKCC1 is important for regulating cell volume, hearing, blood pressure, and regulation of hyperpolarizing GABAergic and glycinergic signaling in the central nervous system. Here, we present a 2.6 Å resolution cryo-electron microscopy structure of human NKCC1 in the substrate-loaded (Na+ , K+ , and 2 Cl- ) and occluded, inward-facing state that has also been observed for the SLC6-type transporters MhsT and LeuT. Cl- binding at the Cl1 site together with the nearby K+ ion provides a crucial bridge between the LeuT-fold scaffold and bundle domains. Cl- -ion binding at the Cl2 site seems to undertake a structural role similar to conserved glutamate of SLC6 transporters and may allow for Cl- -sensitive regulation of transport. Supported by functional studies in mammalian cells and computational simulations, we describe a putative Na+ release pathway along transmembrane helix 5 coupled to the Cl2 site. The results provide insight into the structure-function relationship of NKCC1 with broader implications for other SLC12 family members.
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Affiliation(s)
- Caroline Neumann
- Danish Research Institute of Translational Neuroscience—DANDRITENordic EMBL Partnership for Molecular MedicineAarhusDenmark,Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Rasmus Kock Flygaard
- Danish Research Institute of Translational Neuroscience—DANDRITENordic EMBL Partnership for Molecular MedicineAarhusDenmark,Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Michael Habeck
- Danish Research Institute of Translational Neuroscience—DANDRITENordic EMBL Partnership for Molecular MedicineAarhusDenmark,Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Yong Wang
- Linderstrøm‐Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagenDenmark,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, College of Life SciencesZhejiang UniversityHangzhouChina
| | - Kresten Lindorff‐Larsen
- Linderstrøm‐Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Hans Henrik Gad
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Rune Hartmann
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Joseph Anthony Lyons
- Danish Research Institute of Translational Neuroscience—DANDRITENordic EMBL Partnership for Molecular MedicineAarhusDenmark,Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark,Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityAarhusDenmark
| | | | - Poul Nissen
- Danish Research Institute of Translational Neuroscience—DANDRITENordic EMBL Partnership for Molecular MedicineAarhusDenmark,Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
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12
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 PMCID: PMC9480104 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J. Piper
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M. Johnson
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M. Sexton
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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13
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Thangaratnarajah C, Rheinberger J, Paulino C. Cryo-EM studies of membrane proteins at 200 keV. Curr Opin Struct Biol 2022; 76:102440. [PMID: 36029606 DOI: 10.1016/j.sbi.2022.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
Single-particle cryogenic electron-microscopy (cryo-EM) has emerged as a powerful technique for the structural characterisation of membrane proteins, especially for targets previously thought to be intractable. Taking advantage of the latest hard- and software developments, high-resolution three-dimensional (3D) reconstructions of membrane proteins by cryo-EM has become routine, with 300-kV transmission electron microscopes (TEMs) being the current standard. The use of 200-kV cryo-TEMs is gaining increasingly prominence, showing the capabilities of reaching better than 2 Å resolution for soluble proteins and better than 3 Å resolution for membrane proteins. Here, we highlight the challenges working with membrane proteins and the impact of cryo-EM, and review the technical and practical benefits, achievements and limitations of imaging at lower electron acceleration voltages.
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Affiliation(s)
- Chancievan Thangaratnarajah
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| | - Jan Rheinberger
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands. https://twitter.com/rheinbergerj
| | - Cristina Paulino
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy and Membrane Enzymology Group, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
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14
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Structure of the Human BK Ion Channel in Lipid Environment. MEMBRANES 2022; 12:membranes12080758. [PMID: 36005673 PMCID: PMC9414842 DOI: 10.3390/membranes12080758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023]
Abstract
Voltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage sensing, ligand binding, and channel opening, the structures of ion channels in various functional states and in lipid membrane environments need to be determined. Here, the random spherically constrained (RSC) single-particle cryo-EM method was employed to study human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure was determined at 3.5 Å resolution in the absence of Ca2+. Instead of the common fourfold symmetry observed in ligand-modulated ion channels, a twofold symmetry was observed in hBK in liposomes. Compared with the structure of isolated hSlo1 Ca2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits also moved downwards relative to the two other subunits.
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15
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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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16
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Zhao Y, Shen J, Wang Q, Ruiz Munevar MJ, Vidossich P, De Vivo M, Zhou M, Cao E. Structure of the human cation-chloride cotransport KCC1 in an outward-open state. Proc Natl Acad Sci U S A 2022; 119:e2109083119. [PMID: 35759661 PMCID: PMC9271165 DOI: 10.1073/pnas.2109083119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/25/2022] [Indexed: 12/30/2022] Open
Abstract
Cation-chloride cotransporters (CCCs) catalyze electroneutral symport of Cl- with Na+ and/or K+ across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, maintenance of intracellular Cl- concentration, and neuronal excitability. Here, we present a cryoelectron microscopy structure of human K+-Cl- cotransporter (KCC)1 bound with the VU0463271 inhibitor in an outward-open state. In contrast to many other amino acid-polyamine-organocation transporter cousins, our first outward-open CCC structure reveals that opening the KCC1 extracellular ion permeation path does not involve hinge-bending motions of the transmembrane (TM) 1 and TM6 half-helices. Instead, rocking of TM3 and TM8, together with displacements of TM4, TM9, and a conserved intracellular loop 1 helix, underlie alternate opening and closing of extracellular and cytoplasmic vestibules. We show that KCC1 intriguingly exists in one of two distinct dimeric states via different intersubunit interfaces. Our studies provide a blueprint for understanding the mechanisms of CCCs and their inhibition by small molecule compounds.
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Affiliation(s)
- Yongxiang Zhao
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Jiemin Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Qinzhe Wang
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | | | | | - Marco De Vivo
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Erhu Cao
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
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17
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Moreno E, Plata C, Vazquez N, Oropeza-Víveros DM, Pacheco-Alvarez D, Rojas-Vega L, Olin-Sandoval V, Gamba G. The European and Japanese eel NaCl cotransporter β exhibit chloride currents and are resistant to thiazide type diuretics. Am J Physiol Cell Physiol 2022; 323:C385-C399. [PMID: 35759442 PMCID: PMC9359660 DOI: 10.1152/ajpcell.00213.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The thiazide-sensitive Na+-Cl- cotransporter (NCC) is the major pathway for salt reabsorption in the mammalian distal convoluted tubule, and the inhibition of its function with thiazides is widely used for the treatment of arterial hypertension. In mammals and teleosts, NCC is present as one ortholog that is mainly expressed in the kidney. One exception, however, is the eel, which has two genes encoding NCC. The eNCCa is located in the kidney and eNCCb, which is present in the apical membrane of the rectum. Interestingly, the European eNCCb functions as a NaCl cotransporter that is nevertheless resistant to thiazides and is not activated by low-chloride hypotonic stress. However, in the Japanese eel rectal sac, a thiazide-sensitive NaCl transport mechanism has been described. The protein sequences between eNCCβ and jNCCβ are 98% identical. Here, by site-directed mutagenesis, we transformed eNCCβ into jNCCβ. Our data showed that jNCCβ, similar to eNCCβ, is resistant to thiazides. In addition, both NCCβ proteins have high transport capacity with respect to their renal NCC orthologs, and in contrast to known NCCs, exhibit electrogenic properties that are reduced when residue I172 is substituted by A, G or M. This is considered a key residue for the chloride ion-binding sites of NKCC and KCC. We conclude that NCCb proteins are not sensitive to thiazides and have electrogenic properties dependent on Cl-, and site I172 is important for the function of NCCβ.
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Affiliation(s)
- Erika Moreno
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico
| | - Consuelo Plata
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico
| | - Norma Vazquez
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico.,Molecular Physiology Unit, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tlalpan 14080 Mexico City, Mexico
| | - Dulce María Oropeza-Víveros
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico
| | | | - Lorena Rojas-Vega
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico
| | - Viridiana Olin-Sandoval
- Department of Physiology of Nutrition, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico
| | - Gerardo Gamba
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, 14080 Mexico City, Mexico.,Molecular Physiology Unit, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tlalpan 14080 Mexico City, Mexico
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18
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Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide. Nat Commun 2022; 13:2747. [PMID: 35585053 PMCID: PMC9117670 DOI: 10.1038/s41467-022-30407-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
Cation-chloride cotransporters (CCCs) NKCC1 and NKCC2 catalyze electroneutral symport of 1 Na+, 1 K+, and 2 Cl− across cell membranes. NKCC1 mediates trans-epithelial Cl− secretion and regulates excitability of some neurons and NKCC2 is critical to renal salt reabsorption. Both transporters are inhibited by the so-called loop diuretics including bumetanide, and these drugs are a mainstay for treating edema and hypertension. Here, our single-particle electron cryo-microscopy structures supported by functional studies reveal an outward-facing conformation of NKCC1, showing bumetanide wedged into a pocket in the extracellular ion translocation pathway. Based on these and the previously published inward-facing structures, we define the translocation pathway and the conformational changes necessary for ion translocation. We also identify an NKCC1 dimer with separated transmembrane domains and extensive transmembrane and C-terminal domain interactions. We further define an N-terminal phosphoregulatory domain that interacts with the C-terminal domain, suggesting a mechanism whereby (de)phosphorylation regulates NKCC1 by tuning the strength of this domain association. Loop diuretics including bumetanide inhibit Na+-K+-Cl−-cotransporters (NKCCs) and are used for the treatment of edema and hypertension. Here, Zhao et. al. report structures of NKCC1 with bumetanide bound, revealing its mechanism of action that would facilitate design of novel diuretics.
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19
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The Important Role of Ion Transport System in Cervical Cancer. Int J Mol Sci 2021; 23:ijms23010333. [PMID: 35008759 PMCID: PMC8745646 DOI: 10.3390/ijms23010333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/15/2022] Open
Abstract
Cervical cancer is a significant gynecological cancer and causes cancer-related deaths worldwide. Human papillomavirus (HPV) is implicated in the etiology of cervical malignancy. However, much evidence indicates that HPV infection is a necessary but not sufficient cause in cervical carcinogenesis. Therefore, the cellular pathophysiology of cervical cancer is worthy of study. This review summarizes the recent findings concerning the ion transport processes involved in cell volume regulation and intracellular Ca2+ homeostasis of epithelial cells and how these transport systems are themselves regulated by the tumor microenvironment. For cell volume regulation, we focused on the volume-sensitive Cl− channels and K+-Cl− cotransporter (KCC) family, important regulators for ionic and osmotic homeostasis of epithelial cells. Regarding intracellular Ca2+ homeostasis, the Ca2+ store sensor STIM molecules and plasma membrane Ca2+ channel Orai proteins, the predominant Ca2+ entry mechanism in epithelial cells, are discussed. Furthermore, we evaluate the potential of these membrane ion transport systems as diagnostic biomarkers and pharmacological interventions and highlight the challenges.
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20
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Kacher YG, Karlova MG, Glukhov GS, Zhang H, Zaklyazminskaya EV, Loussouarn G, Sokolova OS. The Integrative Approach to Study of the Structure and Functions of Cardiac Voltage-Dependent Ion Channels. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Portioli C, Ruiz Munevar MJ, De Vivo M, Cancedda L. Cation-coupled chloride cotransporters: chemical insights and disease implications. TRENDS IN CHEMISTRY 2021; 3:832-849. [PMID: 34604727 PMCID: PMC8461084 DOI: 10.1016/j.trechm.2021.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-coupled chloride cotransporters (CCCs) modulate the transport of sodium and/or potassium cations coupled with chloride anions across the cell membrane. CCCs thus help regulate intracellular ionic concentration and consequent cell volume homeostasis. This has been largely exploited in the past to develop diuretic drugs that act on CCCs expressed in the kidney. However, a growing wealth of evidence has demonstrated that CCCs are also critically involved in a great variety of other pathologies, motivating most recent drug discovery programs targeting CCCs. Here, we examine the structure–function relationship of CCCs. By linking recent high-resolution cryogenic electron microscopy (cryo-EM) data with older biochemical/functional studies on CCCs, we discuss the mechanistic insights and opportunities to design selective CCC modulators to treat diverse pathologies. The structural topology and function of all cation-coupled chloride cotransporters (CCCs) have been continuously investigated over the past 40 years, with great progress also thanks to the recent cryogenic electron microscopy (cryo-EM) resolution of the structures of five CCCs. In particular, such studies have clarified the structure–function relationship for the Na-K-Cl cotransporter NKCC1 and K-Cl cotransporters KCC1–4. The constantly growing evidence of the crucial involvement of CCCs in physiological and various pathological conditions, as well as the evidence of their wide expression in diverse body tissues, has promoted CCCs as targets for the discovery and development of new, safer, and more selective/effective drugs for a plethora of pathologies. Post-translational modification anchor points on the structure of CCCs may offer alternative strategies for small molecule drug discovery.
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Affiliation(s)
- Corinne Portioli
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genoa, Italy.,Laboratory of Molecular Modeling and Drug Discovery, IIT, Via Morego, 30 16163 Genoa, Italy
| | | | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, IIT, Via Morego, 30 16163 Genoa, Italy
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genoa, Italy.,Dulbecco Telethon Institute, Via Varese 16b, 00185 Rome, Italy
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22
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Chew TA, Zhang J, Feng L. High-Resolution Views and Transport Mechanisms of the NKCC1 and KCC Transporters. J Mol Biol 2021; 433:167056. [PMID: 34022207 PMCID: PMC9722358 DOI: 10.1016/j.jmb.2021.167056] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/08/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022]
Abstract
Cation-chloride cotransporters (CCCs) are responsible for the coupled co-transport of Cl- with K+ and/or Na+ in an electroneutral manner. They play important roles in myriad fundamental physiological processes--from cell volume regulation to transepithelial solute transport and intracellular ion homeostasis--and are targeted by medicines commonly prescribed to treat hypertension and edema. After several decades of studies into the functions and pharmacology of these transporters, there have been several breakthroughs in the structural determination of CCC transporters. The insights provided by these new structures for the Na+/K+/Cl- cotransporter NKCC1 and the K+/Cl- cotransporters KCC1, KCC2, KCC3 and KCC4 have deepened our understanding of their molecular basis and transport function. This focused review discusses recent advances in the structural and mechanistic understanding of CCC transporters, including architecture, dimerization, functional roles of regulatory domains, ion binding sites, and coupled ion transport.
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Affiliation(s)
- Thomas A Chew
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinru Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liang Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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23
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Chi G, Ebenhoch R, Man H, Tang H, Tremblay LE, Reggiano G, Qiu X, Bohstedt T, Liko I, Almeida FG, Garneau AP, Wang D, McKinley G, Moreau CP, Bountra KD, Abrusci P, Mukhopadhyay SMM, Fernandez‐Cid A, Slimani S, Lavoie JL, Burgess‐Brown NA, Tehan B, DiMaio F, Jazayeri A, Isenring P, Robinson CV, Dürr KL. Phospho-regulation, nucleotide binding and ion access control in potassium-chloride cotransporters. EMBO J 2021; 40:e107294. [PMID: 34031912 PMCID: PMC8280820 DOI: 10.15252/embj.2020107294] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/29/2021] [Accepted: 04/11/2021] [Indexed: 11/26/2022] Open
Abstract
Potassium-coupled chloride transporters (KCCs) play crucial roles in regulating cell volume and intracellular chloride concentration. They are characteristically inhibited under isotonic conditions via phospho-regulatory sites located within the cytoplasmic termini. Decreased inhibitory phosphorylation in response to hypotonic cell swelling stimulates transport activity, and dysfunction of this regulatory process has been associated with various human diseases. Here, we present cryo-EM structures of human KCC3b and KCC1, revealing structural determinants for phospho-regulation in both N- and C-termini. We show that phospho-mimetic KCC3b is arrested in an inward-facing state in which intracellular ion access is blocked by extensive contacts with the N-terminus. In another mutant with increased isotonic transport activity, KCC1Δ19, this interdomain interaction is absent, likely due to a unique phospho-regulatory site in the KCC1 N-terminus. Furthermore, we map additional phosphorylation sites as well as a previously unknown ATP/ADP-binding pocket in the large C-terminal domain and show enhanced thermal stabilization of other CCCs by adenine nucleotides. These findings provide fundamentally new insights into the complex regulation of KCCs and may unlock innovative strategies for drug development.
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Affiliation(s)
- Gamma Chi
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Rebecca Ebenhoch
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
- Present address:
MedChem, Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Henry Man
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
- Present address:
Exscientia LtdOxfordUK
| | - Haiping Tang
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordOxfordUK
| | - Laurence E Tremblay
- Department of MedicineNephrology Research GroupFaculty of MedicineLaval UniversityQuebec CityQCCanada
| | | | - Xingyu Qiu
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordOxfordUK
| | - Tina Bohstedt
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | | | - Alexandre P Garneau
- Department of MedicineNephrology Research GroupFaculty of MedicineLaval UniversityQuebec CityQCCanada
- Cardiometabolic Axis, School of Kinesiology and Physical Activity SciencesUniversity of MontréalMontréalQCCanada
| | - Dong Wang
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Gavin McKinley
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Christophe P Moreau
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Present address:
Celonic AGBaselGermany
| | | | - Patrizia Abrusci
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
- Present address:
Exscientia LtdOxfordUK
| | - Shubhashish M M Mukhopadhyay
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Alejandra Fernandez‐Cid
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Samira Slimani
- Department of MedicineNephrology Research GroupFaculty of MedicineLaval UniversityQuebec CityQCCanada
| | - Julie L Lavoie
- Cardiometabolic Axis, School of Kinesiology and Physical Activity SciencesUniversity of MontréalMontréalQCCanada
| | - Nicola A Burgess‐Brown
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | - Frank DiMaio
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Paul Isenring
- Department of MedicineNephrology Research GroupFaculty of MedicineLaval UniversityQuebec CityQCCanada
| | - Carol V Robinson
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordOxfordUK
| | - Katharina L Dürr
- Nuffield Department of MedicineCentre of Medicines DiscoveryUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNuffield Department of MedicineUniversity of OxfordOxfordUK
- OMass Therapeutics, Ltd.OxfordUK
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24
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Borgogno M, Savardi A, Manigrasso J, Turci A, Portioli C, Ottonello G, Bertozzi SM, Armirotti A, Contestabile A, Cancedda L, De Vivo M. Design, Synthesis, In Vitro and In Vivo Characterization of Selective NKCC1 Inhibitors for the Treatment of Core Symptoms in Down Syndrome. J Med Chem 2021; 64:10203-10229. [PMID: 34137257 PMCID: PMC8311653 DOI: 10.1021/acs.jmedchem.1c00603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intracellular chloride concentration [Cl-]i is defective in several neurological disorders. In neurons, [Cl-]i is mainly regulated by the action of the Na+-K+-Cl- importer NKCC1 and the K+-Cl- exporter KCC2. Recently, we have reported the discovery of ARN23746 as the lead candidate of a novel class of selective inhibitors of NKCC1. Importantly, ARN23746 is able to rescue core symptoms of Down syndrome (DS) and autism in mouse models. Here, we describe the discovery and extensive characterization of this chemical class of selective NKCC1 inhibitors, with focus on ARN23746 and other promising derivatives. In particular, we present compound 40 (ARN24092) as a backup/follow-up lead with in vivo efficacy in a mouse model of DS. These results further strengthen the potential of this new class of compounds for the treatment of core symptoms of brain disorders characterized by the defective NKCC1/KCC2 expression ratio.
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Affiliation(s)
- Marco Borgogno
- Molecular Modeling and Drug Discovery Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Annalisa Savardi
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy.,Dulbecco Telethon Institute, 38123 Rome, Italy
| | - Jacopo Manigrasso
- Molecular Modeling and Drug Discovery Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Alessandra Turci
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy.,Università degli Studi di Genova, via Balbi, 5, 16126 Genoa, Italy
| | - Corinne Portioli
- Molecular Modeling and Drug Discovery Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy.,Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Andrea Contestabile
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy.,Dulbecco Telethon Institute, 38123 Rome, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Laboratory, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genoa, Italy
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25
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Delpire E. Advances in the development of novel compounds targeting cation-chloride cotransporter physiology. Am J Physiol Cell Physiol 2021; 320:C324-C340. [PMID: 33356948 PMCID: PMC8294628 DOI: 10.1152/ajpcell.00566.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/05/2023]
Abstract
For about half a century, the pharmacology of electroneutral cation-chloride cotransporters has been dominated by a few drugs that are widely used in clinical medicine. Because these diuretic drugs are so good at what they do, there has been little incentive in expanding their pharmacology. The increasing realization that cation-chloride cotransporters are involved in many other key physiological processes and the knowledge that different tissues express homologous proteins with matching transport functions have rekindled interest in drug discovery. This review summarizes the methods available to assess the function of these transporters and describe the multiple efforts that have made to identify new compounds. We describe multiple screens targeting KCC2 function and one screen designed to find compounds that discriminate between NKCC1 and NKCC2. Two of the KCC2 screens identified new inhibitors that are 3-4 orders of magnitude more potent than furosemide. Additional screens identified compounds that purportedly increase cell surface expression of the cotransporter, as well as several FDA-approved drugs that increase KCC2 transcription and expression. The technical details of each screen biased them toward specific processes in the life cycle of the transporter, making these efforts independent and complementary. In addition, each drug discovery effort contributes to our understanding of the biology of the cotransporters.
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Affiliation(s)
- Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, Tennessee
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26
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Virtanen MA, Uvarov P, Mavrovic M, Poncer JC, Kaila K. The Multifaceted Roles of KCC2 in Cortical Development. Trends Neurosci 2021; 44:378-392. [PMID: 33640193 DOI: 10.1016/j.tins.2021.01.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
KCC2, best known as the neuron-specific chloride-extruder that sets the strength and polarity of GABAergic currents during neuronal maturation, is a multifunctional molecule that can regulate cytoskeletal dynamics via its C-terminal domain (CTD). We describe the molecular and cellular mechanisms involved in the multiple functions of KCC2 and its splice variants, ranging from developmental apoptosis and the control of early network events to the formation and plasticity of cortical dendritic spines. The versatility of KCC2 actions at the cellular and subcellular levels is also evident in mature neurons during plasticity, disease, and aging. Thus, KCC2 has emerged as one of the most important molecules that shape the overall neuronal phenotype.
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Affiliation(s)
- Mari A Virtanen
- Molecular and Integrative Biosciences, University of Helsinki, 00014 Helsinki, Finland; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Pavel Uvarov
- Molecular and Integrative Biosciences, University of Helsinki, 00014 Helsinki, Finland; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Martina Mavrovic
- Molecular and Integrative Biosciences, University of Helsinki, 00014 Helsinki, Finland; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland; Department of Molecular Medicine, University of Oslo, 0372 Oslo, Norway
| | - Jean Christophe Poncer
- INSERM, UMRS 1270, 75005 Paris, France; Sorbonne Université, 75005 Paris, France; Institut du Fer à Moulin, 75005 Paris, France
| | - Kai Kaila
- Molecular and Integrative Biosciences, University of Helsinki, 00014 Helsinki, Finland; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland.
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27
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Zhang S, Zhou J, Zhang Y, Liu T, Friedel P, Zhuo W, Somasekharan S, Roy K, Zhang L, Liu Y, Meng X, Deng H, Zeng W, Li G, Forbush B, Yang M. The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2. Commun Biol 2021; 4:226. [PMID: 33597714 PMCID: PMC7889885 DOI: 10.1038/s42003-021-01750-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 01/22/2021] [Indexed: 11/08/2022] Open
Abstract
NKCC and KCC transporters mediate coupled transport of Na++K++Cl- and K++Cl- across the plasma membrane, thus regulating cell Cl- concentration and cell volume and playing critical roles in transepithelial salt and water transport and in neuronal excitability. The function of these transporters has been intensively studied, but a mechanistic understanding has awaited structural studies of the transporters. Here, we present the cryo-electron microscopy (cryo-EM) structures of the two neuronal cation-chloride cotransporters human NKCC1 (SLC12A2) and mouse KCC2 (SLC12A5), along with computational analysis and functional characterization. These structures highlight essential residues in ion transport and allow us to propose mechanisms by which phosphorylation regulates transport activity.
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Affiliation(s)
- Sensen Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jun Zhou
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Perrine Friedel
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Suma Somasekharan
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kasturi Roy
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenwen Zeng
- Center for Life Sciences, Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Biff Forbush
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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28
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Abstract
The SARS-CoV-2 3a protein is a putative ion channel implicated in virus life cycle and pathogenesis. We recently expressed, purified, and reconstituted 3a into lipid nanodiscs to solve its structure by cryo-EM to 2.1Å resolution. In this chapter, we describe methods we developed in order to facilitate the study of this protein in other laboratories. We emphasize factors that enabled rapid progression from gene sequence to reconstituted protein (3 weeks in the case of 3a) and provide general observations and tips for adapting these protocols to other membrane proteins of interest.
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Affiliation(s)
- David M Kern
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States; Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, United States; California Institute for Quantitative Biology (QB3), University of California Berkeley, Berkeley, CA, United States
| | - Stephen G Brohawn
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States; Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, United States; California Institute for Quantitative Biology (QB3), University of California Berkeley, Berkeley, CA, United States.
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29
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Hartmann AM, Fu L, Ziegler C, Winklhofer M, Nothwang HG. Structural changes in the extracellular loop 2 of the murine KCC2 potassium chloride cotransporter modulate ion transport. J Biol Chem 2021; 296:100793. [PMID: 34019872 PMCID: PMC8191313 DOI: 10.1016/j.jbc.2021.100793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 01/22/2023] Open
Abstract
K+-Cl- cotransporters (KCCs) play important roles in physiological processes such as inhibitory neurotransmission and cell-volume regulation. KCCs exhibit significant variations in K+ affinities, yet recent atomic structures demonstrated that K+- and Cl--binding sites are highly conserved, raising the question of whether additional structural elements may contribute to ion coordination. The termini and the large extracellular domain (ECD) of KCCs exhibit only low sequence identity and were already discussed as modulators of transport activity. Here, we used the extracellular loop 2 (EL2) that links transmembrane helices (TMs) 3 and 4, as a mechanism to modulate ECD folding. We compared consequences of point mutations in the K+-binding site on the function of WT KCC2 and in a KCC2 variant, in which EL2 was structurally altered by insertion of a IFYPYDVPDYAGYPYDVPDYAGSYPYDVPDYAAHAAA (3xHA) tag (36 amino acids). In WT KCC2, individual mutations of five residues in the K+-binding site resulted in a 2- to 3-fold decreased transport rate. However, the same mutations in the KCC2 variant with EL2 structurally altered by insertion of a 3xHA tag had no effect on transport activity. Homology models of mouse KCC2 with the 3xHA tag inserted into EL2 using ab initio prediction were generated. The models suggest subtle conformational changes occur in the ECD upon EL2 modification. These data suggest that a conformational change in the ECD, for example, by interaction with EL2, might be an elegant way to modulate the K+ affinity of the different isoforms in the KCC subfamily.
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Affiliation(s)
- Anna-Maria Hartmann
- Division of Neurogenetics, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Research Center for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Lifei Fu
- Biophysics II, Biophysics II-Structural Biology, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Christine Ziegler
- Biophysics II, Biophysics II-Structural Biology, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Michael Winklhofer
- Institute for Biology and Environmental Sciences IBU, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Hans Gerd Nothwang
- Division of Neurogenetics, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Research Center for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany; Center of Excellence Hearing4all, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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30
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Xie Y, Chang S, Zhao C, Wang F, Liu S, Wang J, Delpire E, Ye S, Guo J. Structures and an activation mechanism of human potassium-chloride cotransporters. SCIENCE ADVANCES 2020; 6:eabc5883. [PMID: 33310850 PMCID: PMC7732191 DOI: 10.1126/sciadv.abc5883] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/21/2020] [Indexed: 05/07/2023]
Abstract
Potassium-chloride cotransporters KCC1 to KCC4 mediate the coupled export of potassium and chloride across the plasma membrane and play important roles in cell volume regulation, auditory system function, and γ-aminobutyric acid (GABA) and glycine-mediated inhibitory neurotransmission. Here, we present 2.9- to 3.6-Å resolution structures of full-length human KCC2, KCC3, and KCC4. All three KCCs adopt a similar overall architecture, a domain-swap dimeric assembly, and an inward-facing conformation. The structural and functional studies reveal that one unexpected N-terminal peptide binds at the cytosolic facing cavity and locks KCC2 and KCC4 at an autoinhibition state. The C-terminal domain (CTD) directly interacts with the N-terminal inhibitory peptide, and the relative motions between the CTD and the transmembrane domain (TMD) suggest that CTD regulates KCCs' activities by adjusting the autoinhibitory effect. These structures provide the first glimpse of full-length structures of KCCs and an autoinhibition mechanism among the amino acid-polyamine-organocation transporter superfamily.
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Affiliation(s)
- Yuan Xie
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shenghai Chang
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Cheng Zhao
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Feng Wang
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng West Road, Jiangyin, 214437, China
| | - Si Liu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jin Wang
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China.
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiangtao Guo
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
- Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
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31
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Koumangoye R, Bastarache L, Delpire E. NKCC1: Newly Found as a Human Disease-Causing Ion Transporter. FUNCTION 2020; 2:zqaa028. [PMID: 33345190 PMCID: PMC7727275 DOI: 10.1093/function/zqaa028] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 01/06/2023] Open
Abstract
Among the electroneutral Na+-dependent chloride transporters, NKCC1 had until now evaded identification as a protein causing human diseases. The closely related SLC12A transporters, NKCC2 and NCC have been identified some 25 years ago as responsible for Bartter and Gitelman syndromes: two renal-dependent salt wasting disorders. Absence of disease was most surprising since the NKCC1 knockout mouse was shown in 1999 to be viable, albeit with a wide range of deleterious phenotypes. Here we summarize the work of the past 5 years that introduced us to clinical cases involving NKCC1. The most striking cases are of 3 children with inherited mutations, who have complete absence of NKCC1 expression. These cases establish that lack of NKCC1 causes deafness; CFTR-like secretory defects with mucus accumulation in lung and intestine; severe xerostomia, hypotonia, dysmorphic facial features, and severe neurodevelopmental disorder. Another intriguing case is of a patient with a dominant deleterious SLC12A2 allele. This de novo mutation introduced a premature stop codon leading to a truncated protein. This mutant transporter seems to exert dominant-negative effect on wild-type transporter only in epithelial cells. The patient who suffers from lung, bladder, intestine, pancreas, and multiple endocrine abnormalities has, however, normal hearing and cognition. Finally, new reports substantiate the haploinsufficiency prediction of the SLC12A2 gene. Cases with single allele mutations in SLC12A2 have been linked to hearing loss and neurodevelopmental disorders.
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Affiliation(s)
- Rainelli Koumangoye
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Corresponding author. E-mail:
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32
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Wu M, Lander GC. How low can we go? Structure determination of small biological complexes using single-particle cryo-EM. Curr Opin Struct Biol 2020; 64:9-16. [PMID: 32599507 PMCID: PMC7666008 DOI: 10.1016/j.sbi.2020.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022]
Abstract
For decades, high-resolution structural studies of biological macromolecules with masses of <200kDa by cryo-EM single-particle analysis were considered infeasible. It was not until several years after the advent of direct detectors that the overlooked potential of cryo-EM for studying small complexes was first realized. Subsequent advances in sample preparation, imaging, and data processing algorithms have improved our ability to visualize small biological targets. In the past two years alone, nearly two hundred high-resolution structures have been determined of small (<200kDa) macromolecules, the smallest being approximately 39kDa in molecular weight. Here we summarize some salient lessons and strategies for cryo-EM studies of small biological complexes, and also consider future prospects for routine structure determination.
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Affiliation(s)
- Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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33
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Reid MS, Kern DM, Brohawn SG. Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs. eLife 2020; 9:e52505. [PMID: 32286222 PMCID: PMC7200160 DOI: 10.7554/elife.52505] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 04/12/2020] [Indexed: 01/24/2023] Open
Abstract
Cation-chloride-cotransporters (CCCs) catalyze transport of Cl- with K+ and/or Na+across cellular membranes. CCCs play roles in cellular volume regulation, neural development and function, audition, regulation of blood pressure, and renal function. CCCs are targets of clinically important drugs including loop diuretics and their disruption has been implicated in pathophysiology including epilepsy, hearing loss, and the genetic disorders Andermann, Gitelman, and Bartter syndromes. Here we present the structure of a CCC, the Mus musculus K+-Cl- cotransporter (KCC) KCC4, in lipid nanodiscs determined by cryo-EM. The structure, captured in an inside-open conformation, reveals the architecture of KCCs including an extracellular domain poised to regulate transport activity through an outer gate. We identify binding sites for substrate K+ and Cl- ions, demonstrate the importance of key coordinating residues for transporter activity, and provide a structural explanation for varied substrate specificity and ion transport ratio among CCCs. These results provide mechanistic insight into the function and regulation of a physiologically important transporter family.
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Affiliation(s)
- Michelle S Reid
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
| | - David M Kern
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
| | - Stephen Graf Brohawn
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Helen Wills Neuroscience Institute, University of California BerkeleyBerkeleyUnited States
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34
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Cianfrocco MA, Kellogg EH. What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models. J Chem Inf Model 2020; 60:2458-2469. [PMID: 32078321 DOI: 10.1021/acs.jcim.9b01178] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an increased number of microscopes, cryo-EM facilities, and scientists eager to leverage the ability to determine protein structures without crystallization. However, numerous pitfalls and considerations beset the path toward high-resolution structures and are not necessarily obvious from literature surveys. Here, we detail the most common misconceptions when initiating a cryo-EM project and common technical hurdles, as well as their solutions, and we conclude with a vision for the future of this exciting field.
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Affiliation(s)
- Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics,Cornell University, Ithaca, New York 14850, United States
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